Brookstone, the ubiquitous seller of cool but largely unneeded things, has filed for Chapter 11 bankruptcy protection again and will close the 101 of its stores that are located in malls.

Malls have suffered for years due to far-reaching shifts in the way that Americans shop for just about everything, which has diminished foot traffic at Brookstone. On Thursday, CEO Piau Phang Foo called the situation in malls “extremely challenging,” and thanked employees who had staffed stores in those...